Modified interferon beta with reduced immunogenicity

ABSTRACT

A modified interferon beta (INFβ) is provided, which is less immunogenic than human INFβ (SEQ ID NO: 1) when administered to a human in vivo. The modified INFβ comprises an amino acid residue sequence that differs from SEQ ID NO: 1 by a substitution at one or more residues of SEQ ID NO: 1. Preferred substitutions are at residues selected from the group consisting of residue 50, 59, 60, 62, 63, 66, 67, 69, 70, 125, 126, 129, 130, 132, 133, and 138. Examples of suitable substitutions include F50A, L57A, I59A, Y60N, M62A, L63A, I66T, F67H, I69A, F70A, Y125A, Y126A, I129A, L130A, Y132S, L133A, Y138H, and Y138A.

This application is the National Stage of International Application No.PCT/EP02/02925, filed on Mar. 15, 2002, which claims priority fromEuropean Patent Application No. 01106539.8, filed on Mar. 15, 2001.

FIELD OF THE INVENTION

The present invention relates to polypeptides to be administeredespecially to humans and in particular for therapeutic use. Thepolypeptides are modified polypeptides whereby the modification resultsin a reduced propensity for the polypeptide to elicit an immune responseupon administration to the human subject. The invention in particularrelates to the modification of human interferon and specifically humaninterferon beta (INFβ) to result in INFβ protein variants that aresubstantially non-immunogenic or less immunogenic than any non-modifiedcounterpart when used in vivo. The invention relates furthermore toT-cell epitope peptides derived from said non-modified protein by meansof which it is possible to create modified INFβ variants with reducedimmunogenicity.

BACKGROUND OF THE INVENTION

There are many instances whereby the efficacy of a therapeutic proteinis limited by an unwanted immune reaction to the therapeutic protein.Several mouse monoclonal antibodies have shown promise as therapies in anumber of human disease settings but in certain cases have failed due tothe induction of significant degrees of a human anti-murine antibody(HAMA) response [Schroff, R. W. et al (1985) Cancer Res. 45: 879-885;Shawler, D. L. et al (1985) J. Immunol. 135: 1530-1535]. For monoclonalantibodies, a number of techniques have been developed in attempt toreduce the HAMA response [WO 89/09622; EP 0239400; EP 0438310; WO91/06667]. These recombinant DNA approaches have generally reduced themouse genetic information in the final antibody construct whilstincreasing the human genetic information in the final construct.Notwithstanding, the resultant “humanized” antibodies have, in severalcases, still elicited an immune response in patients [Issacs J. D.(1990) Sem. Immunol. 2:449, 456; Rebello, P. R. et al (1999)Transplantation 68: 1417-1420].

Antibodies are not the only class of polypeptide molecule administeredas a therapeutic agent against which an immune response may be mounted.Even proteins of human origin and with the same amino acid sequences asoccur within humans can still induce an immune response in humans.Notable examples include the therapeutic use of granulocyte-macrophagecolony stimulating factor [Wadhwa, M. et al (1999) Clin. Cancer Res. 5:1353-1361] and interferon alpha 2 [Russo, D. et al (1996) Bri. J. Haem.94: 300-305; Stein, R. et al (1988) New Engl. J. Med. 318: 1409-1413]amongst others.

A principal factor in the induction of an immune response is thepresence within the protein of peptides that can stimulate the activityof T-cells via presentation on MHC class II molecules, so-called “T-cellepitopes”. Such potential T-cell epitopes are commonly defined as anyamino acid residue sequence with the ability to bind to MHC Class IImolecules. Such T-cell epitopes can be measured to establish MHCbinding. Implicitly, a “T-cell epitope” means an epitope which whenbound to MHC molecules can be recognized by a T-cell receptor (TCR), andwhich can, at least in principle, cause the activation of these T-cellsby engaging a TCR to promote a T-cell response. It is, however, usuallyunderstood that certain peptides which are found to bind to MHC Class IImolecules may be retained in a protein sequence because such peptidesare recognized as “self” within the organism into which the finalprotein is administered.

It is known, that certain of these T-cell epitope peptides can bereleased during the degradation of peptides, polypeptides or proteinswithin cells and subsequently be presented by molecules of the majorhistocompatability complex (MHC) in order to trigger the activation ofT-cells. For peptides presented by MHC Class II, such activation ofT-cells can then give rise, for example, to an antibody response bydirect stimulation of B-cells to produce such antibodies.

MHC Class II molecules are a group of highly polymorphic proteins whichplay a central role in helper T-cell selection and activation. The humanleukocyte antigen group DR (HLA-DR) are the predominant isotype of thisgroup of proteins and are the major focus of the present invention.However, isotypes HLA-DQ and HLA-DP perform similar functions, hence thepresent invention is equally applicable to these. The MHC class II DRmolecule is made of an alpha and a beta chain which insert at theirC-termini through the cell membrane. Each hetero-dimer possesses aligand binding domain which binds to peptides varying between 9 and 20amino acids in length, although the binding groove can accommodate amaximum of 11 amino acids. The ligand binding domain is comprised ofamino acids 1 to 85 of the alpha chain, and amino acids 1 to 94 of thebeta chain. DQ molecules have recently been shown to have an homologousstructure and the DP family proteins are also expected to be verysimilar. In humans approximately 70 different allotypes of the DRisotype are known, for DQ there are 30 different allotypes and for DP 47different allotypes are known. Each individual bears two to four DRalleles, two DQ and two DP alleles. The structure of a number of DRmolecules has been solved and such structures point to an open-endedpeptide binding groove with a number of hydrophobic pockets which engagehydrophobic residues (pocket residues) of the peptide [Brown et alNature (1993) 364:33; Stern et al (1994) Nature 368:215]. Polymorphismidentifying the different allotypes of class II molecule contributes toa wide diversity of different binding surfaces for peptides within thepeptide binding grove and at the population level ensures maximalflexibility with regard to the ability to recognize foreign proteins andmount an immune response to pathogenic organisms.

There is a considerable amount of polymorphism within the ligand bindingdomain with distinct “families” within different geographicalpopulations and ethnic groups. This polymorphism affects the bindingcharacteristics of the peptide binding domain, thus different “families”of DR molecules will have specificities for peptides with differentsequence properties, although there may be some overlap. Thisspecificity determines recognition of Th-cell epitopes (Class II T-cellresponse) which are ultimately responsible for driving the antibodyresponse to B-cell epitopes present on the same protein from which theTh-cell epitope is derived. Thus, the immune response to a protein in anindividual is heavily influenced by T-cell epitope recognition which isa function of the peptide binding specificity of that individual'sHLA-DR allotype. Therefore, in order to identify T-cell epitopes withina protein or peptide in the context of a global population, it isdesirable to consider the binding properties of as diverse a set ofHLA-DR allotypes as possible, thus covering as high a percentage of theworld population as possible.

An immune response to a therapeutic protein such as INFβ proceeds viathe MHC class II peptide presentation pathway. Here exogenous proteinsare engulfed and processed for presentation in association with MHCclass II molecules of the DR, DQ or DP type. MHC Class II molecules areexpressed by professional antigen presenting cells (APCs), such asmacrophages and dendritic cells amongst others. Engagement of a MHCclass II peptide complex by a cognate T-cell receptor on the surface ofthe T-cell, together with the cross-binding of certain otherco-receptors such as the CD4 molecule, can induce an activated statewithin the T-cell. Activation leads to the release of cytokines furtheractivating other lymphocytes such as B cells to produce antibodies oractivating T killer cells as a full cellular immune response.

The ability of a peptide to bind a given MHC class II molecule forpresentation on the surface of an APC is dependent on a number offactors most notably its primary sequence. This will influence both itspropensity for proteolytic cleavage and also its affinity for bindingwithin the peptide binding cleft of the MHC class II molecule. The MHCclass II/peptide complex on the APC surface presents a binding face to aparticular T-cell receptor (TCR) able to recognize determinants providedboth by exposed residues of the peptide and the MHC class II molecule.

In the art there are procedures for identifying synthetic peptides ableto bind MHC class II molecules (e.g. WO98/52976 and WO00/34317). Suchpeptides may not function as T-cell epitopes in all situations,particularly, in vivo due to the processing pathways or other phenomenaT-cell epitope identification is the first step to epitope elimination.The identification and removal of potential T-cell epitopes fromproteins has been previously disclosed. In the art methods have beenprovided to enable the detection of T-cell epitopes usually bycomputational means scanning for recognized sequence motifs inexperimentally determined T-cell epitopes or alternatively usingcomputational techniques to predict MHC class II-binding peptides and inparticular DR-binding peptides.

WO98/52976 and WO00/34317 teach computational threading approaches toidentifying polypeptide sequences with the potential to bind a sub-setof human MHC class II DR allotypes. In these teachings, predicted T-cellepitopes are removed by the use of judicious amino acid substitutionwithin the primary sequence of the therapeutic antibody or non-antibodyprotein of both non-human and human derivation.

Other techniques exploiting soluble complexes of recombinant MHCmolecules in combination with synthetic peptides and able to bind toT-cell clones from peripheral blood samples from human or experimentalanimal subjects have been used in the art [Kern, F. et al (1998) NatureMedicine 4:975-978; Kwok, W. W. et al (2001) TRENDS in Immunol.22:583-588]. These and other schemes including for example the use ofwhole INFβ proteins or INFβ derived synthetic peptides or variantmolecules thereof which are screened for molecules with altered abilityto bind or stimulate T-cells may also be exploited in an epitopeidentification strategy.

As depicted above and as consequence thereof, it would be desirable toidentify and to remove or at least to reduce T-cell epitopes from agiven in principal therapeutically valuable but originally immunogenicpeptide, polypeptide or protein.

One of these therapeutically valuable molecules is INFβ. The molecule isa single chain glycoprotein of 166 amino acid residues with importantbiological and immunological activity. The protein has significanttherapeutic potential in man as an anti-viral, anti-proliferative andimmunomodulating agent. There are a number of commercial sources ofrecombinant INFβ and these include AVONE® recombinant INFβ; manufacturedby Biogen, Inc. (Cambridge, MA, USA); REBIF® recombinantINFβmanufactured by Serono Intemationa (Geneva, Switzerland) andBETASERON® recombinant INFβ produced by the Chiron Corporation(Emeryville, Calif, USA). The amino acid sequences of AVONEX®recombinant INFβ and REBIF® recombinant INFβ are identical to that ofnatural human INFβ and both products are glycosylated. By contrast,BETASERON® recombinant INFβ is produced from an E.coli expression hostand is a mutated form of INFβ where cysteine 17 has been mutated to aserine residue. It is a 165 amino acid non-glycosylated protein with amolecular weight of 18500.

The mature human INFβ protein is single polypeptide of 166 amino acidswith a molecular weight of 22500 and is produced by various cell typesincluding fibroblasts and macrophages. The amino acid sequence of humanINFβ (depicted as one-letter code) is as follows:

(SEQ ID NO: 1) MSYNLLGFLQRSSNFQCQKLLWQLNGRLEYCLKDRMNFDIPEEIKQLQQFQKEDAALTIYEMLQNIFAIFRQDSSSTGWNETIVENLLANVYHQINHLKβTVLEEKLEKEDFTRGKLMSSLHLKRYYGRILHYLKAKEYSHCAWTIVRVEILR NFYFINRLTGYLRN.

Others have provided INFβ molecules, including modified IFNβ such as themutated and aglycosylated form comprising Betaseron® and the series ofalanine scanning mutants described by Runkel et al [Runkel, L. Et al(2000) Biochemistry 39: 2538-2551]. Other examples include thosedisclosed in U.S. Pat. No. 4,588,585 and U.S. Pat. No. 6,127,332 butnone of these teachings recognise the importance of T cell epitopes tothe immunogenic properties of the protein nor have been conceived todirectly influence said properties in a specific and controlled wayaccording to the scheme of the present invention.

However, there is a continued need for INFβ analogues with enhancedproperties. Desired enhancements include alternative schemes andmodalities for the expression and purification of the said therapeutic,but also and especially, improvements in the biological properties ofthe protein. There is a particular need for enhancement of the in vivocharacteristics when administered to the human subject. In this regard,it is highly desired to provide INFβ with reduced or absent potential toinduce an immune response in the human subject.

SUMMARY AND DESCRIPTION OF THE INVENTION

The present invention provides for modified forms of human interferonbeta 1a, herein called “INFβ”, in which the immune characteristic ismodified by means of reduced or removed numbers of potential T-cellepitopes.

The invention discloses sequences identified within the INFβ primarysequence that are potential T-cell epitopes by virtue of MHC class IIbinding potential. This disclosure specifically pertains the human INFβprotein being 166 amino acid residues.

The invention discloses also specific positions within the primarysequence of the molecule which according to the invention are to bealtered by specific amino acid substitution, addition or deletion whilstretaining to a maximum degree the biological activity of the protein. Incases in which the loss of immunogenicity can be achieved only by asimultaneous loss of biological activity it is possible to restore saidactivity by further alterations within the amino acid sequence of theprotein.

The invention furthermore discloses methods to produce such modifiedmolecules, and above all methods to identify said T-cell epitopes whichrequire alteration in order to reduce or remove immunogenic sites.

The protein according to this invention would expect to display anincreased circulation time within the human subject and would be ofparticular benefit in chronic or recurring disease settings such as isthe case for a number of indications for INFβ. The present inventionprovides for modified forms of INFβ proteins that are expected todisplay enhanced properties in vivo. The present invention discloses themajor regions of the INFβ primary sequence that are immunogenic in manand provides modification to the said sequences to eliminate or reducethe immunogenic effectiveness of these sites. In one embodiment,synthetic peptides comprising the said immunogenic regions can beprovided in pharmaceutical composition for the purpose of promoting atolerogenic response to the whole molecule. In a further embodiment, themodified INFβ molecules of the present invention can be used inpharmaceutical compositions.

In summary the invention relates to the following issues:

-   -   a modified molecule having the biological activity of lNFβ and        being substantially non-immunogenic or less immunogenic than any        non-modified molecule having the same biological activity when        used in vivo;    -   an accordingly specified molecule, wherein said loss of        immunogenicity is achieved by removing one or more T-cell        epitopes derived from the originally non-modified molecule;    -   an accordingly specified molecule, wherein said loss of        immunogenicity is achieved by reduction in numbers of MHC        allotypes able to bind peptides derived from said molecule;    -   an accordingly specified molecule, wherein one T-cell epitope is        removed;    -   an accordingly specified molecule, wherein said originally        present T-cell epitopes are MHC class II ligands or peptide        sequences which show the ability to stimulate or bind T-cells        via presentation on class II;    -   an accordingly specified molecule, wherein said peptide        sequences are selected from the group as depicted in FIG. 1;    -   an accordingly specified molecule, wherein 1-9 amino acid        residues, preferably one amino acid residue in any of the        originally present T-cell epitopes are altered;    -   an accordingly specified molecule, wherein the alteration of the        amino acid residues is substitution, addition or deletion of        originally present amino acid(s) residue(s) by other amino acid        residue(s) at specific position(s);    -   an accordingly specified molecule, wherein one or more of the        amino acid residue substitutions are carried out as indicated in        FIG. 2;    -   an accordingly specified molecule, wherein (additionally) one or        more of the amino acid residue substitutions are carried out as        indicated in FIG. 3 for the reduction in the number of MHC        allotypes able to bind peptides derived from said molecule;    -   an accordingly specified molecule, wherein one or more amino        acid residue substitutions are carried out as indicted in FIG.        4.    -   an accordingly specified molecule, wherein, if necessary,        additionally further alteration usually by substitution,        addition or deletion of specific amino acid(s) is conducted to        restore biological activity of said molecule;    -   an accordingly specified molecule wherein alteration is        conducted at one or more residues from the string of contiguous        residues of sequence (a) QFQKEDAALTIYEMLQNIFAIFRQ (R1; SEQ ID        NO: 2) and/or of sequence; (b) RYYGRILHYLKAKEYSHCAWT (R2; SEQ ID        NO: 3) wherein said sequences are derived from the INFβ        wild-type sequence;    -   a peptide molecule comprising 13-15 consecutive residues from        any of sequences (a) or (b) above;    -   a peptide molecule comprising at least 9 consecutive residues        from any of the sequences (a) or (b) above;    -   a peptide molecule of above sharing greater than 90% amino acid        identity with any of the peptide sequences derived from (a)        or (b) above;    -   a peptide molecule of above sharing greater than 80% amino acid        identity with any of the peptide sequences derived from (a)        or (b) above;    -   peptide sequences as above able to bind MHC class II;    -   an accordingly specified INFβ molecule, wherein one or more of        the amino acid substitutions is conducted at a position        corresponding to any of the amino acids specified within        sequence (a) above;    -   an accordingly specified INFβ molecule, wherein one or more of        the amino acid substitutions is conducted at a position        corresponding to any of the amino acids specified within        sequence (b) above;    -   an accordingly specified INFβ molecule, wherein one or more of        the amino acid substitutions is conducted at a position        corresponding to any of the amino acids specified within        sequences (a) or (b) above;    -   a modified human interferon beta (INFβ) having reduced        immunogenicity consisting of the following sequence:

(SEQ ID NO:4) MSYNLLGFLQRSSNFQX⁰QKLLWQLNGRLEYCLKDRMNFDIPEEIKQLQQX¹QKEDAAX²TX³X⁴EX⁵X⁶QNX⁷X⁸AX⁹X¹⁰RQDSSSTGWNETIVENLLANVYHQINHLKTVLEEKLEKEDFTRGKLMSSLHLKRYYGRILHYLKAKEYSHCAWTIVRVEILRNFYFINRLTGYLRN,

-   -   wherein X⁰ is C, S; X¹ is F, A; X² is L, A; X³ is I, A; X⁴ is Y,        N; X⁵ is M, A; X⁶ is L, A; X⁷ is I, T; X⁸ is F, H; X⁹ is I, A        and X¹⁰ is F, A;    -   whereby simultaneously X^(1=F, X) ²=L, X³=I, X⁴=Y, X⁵=M, X⁶=L,        X⁷=I, X^(8=F, X) ⁹=I and X¹⁰=F are excluded (these exclusions        describe the known imungenetically non-modified INFβ variants);    -   a modified human interferon beta (INFβ) having reduced        immunogenicity consisting of the following sequence:

(SEQ ID NO:5) MSYNLLGFLQRSSNFQX⁰QKLLWQLNGRLEYCLKDRMNFDIPEEIKQLQQFQKEDAALTIYEMLQNIFAIFRQDSSSTGWNETIVENLLANVYHQINHLKTVLEEKLEKEDFTRGKLMSSLHLKRX¹X²GRX³X⁴HX⁵X⁶KAKEX⁷SHCAWTIVRVEILRNFYFINRLTGYLRN,

-   -   wherein X⁰ is C, S; X^(l) is Y, A; X² is Y, A; X³ is I, A; X⁴ is        L, A; X⁵ is Y, S; X⁶ is L, A and X⁷ is Y, H, A; whereby        simultaneously X¹=Y, X² =Y, X³ =I, X⁴ =L, X⁵ =Y, X⁶ =L and X⁷ =Y        are excluded. (these exclusions describe the known        imungenetically non-modified INFβ variants);    -   an INF beta molecule consisting of 9-15 consecutive amino acid        residues, having a potential MHC class II binding activity and        created from the primary sequence of non-modified INEβ, whereby        said molecule has a stimulation index of at least at least 1.8,        preferably 1.8-2, more preferably>2, in a biological assay of        cellular proliferation wherein said index is taken as the value        of cellular proliferation scored following stimulation by a        peptide and divided by the value of cellular proliferation        scored in control cells not in receipt peptide and wherein        cellular proliferation is measured by any suitable means;    -   a pharmaceutical composition comprising any of the peptides or        modified peptides of above having the activity of binding to MHC        class II;    -   a DNA sequence or molecule which codes for any of said specified        modified molecules as defined above and below;    -   a pharmaceutical composition comprising a modified molecule        having the biological activity of INFβ;    -   a pharmaceutical composition as defined above and/or in the        claims, optionally together with a pharmaceutically acceptable        carrier, diluent or excipient;    -   a method for manufacturing a modified molecule having the        biological activity of INFβ as defined in any of the claims of        the above-cited claims comprising the following steps:    -   (i) determining the amino acid sequence of the polypeptide or        part thereof; (ii) identifying one or more potential T-cell        epitopes within the amino acid sequence of the protein by any        method including determination of the binding of the peptides to        MHC molecules using in vitro or in silico techniques or        biological assays; (iii) designing new sequence variants with        one or more amino acids within the identified potential T-cell        epitopes modified in such a way to substantially reduce or        eliminate the activity of the T-cell epitope as determined by        the binding of the peptides to MHC molecules using in vitro or        in silico techniques or biological assays; (iv) constructing        such sequence variants by recombinant DNA techniques and testing        said variants in order to identify one or more variants with        desirable properties; and (v) optionally repeating steps        (ii)-(iv);    -   an accordingly specified method, wherein step (iii) is carried        out by substitution, addition or deletion of 1-9 amino acid        residues in any of the originally present T-cell epitopes;    -   an accordingly specified method, wherein the alteration is made        with reference to an homologous protein sequence and/or in        si/icc modeling techniques;    -   an accordingly specified method, wherein step (ii) of above is        carried out by the following steps: (a) selecting a region of        the peptide having a known amino acid residue sequence; (b)        sequentially sampling overlapping amino acid residue segments of        predetermined uniform size and constituted by at least three        amino acid residues from the selected region; (c) calculating        MHC Class II molecule binding score for each said sampled        segment by summing assigned values for each hydrophobic amino        acid residue side chain present in said sampled amino acid        residue segment; and (d) identifying at least one of said        segments suitable for modification, based on the calculated MHC        Class II molecule binding score for that segment, to change        overall MHC Class II binding score for the peptide without        substantially reducing therapeutic utility of the peptide;        step (c) is preferably carried out by using a Böhm scoring        function modified to include 12-6 van der Waal's ligand-protein        energy repulsive term and ligand conformational energy term        by (1) providing a first data base of MHC Class II molecule        models; (2) providing a second data base of allowed peptide        backbones for said MHC Class II molecule models; (3) selecting a        model from said first data base; (4) selecting an allowed        peptide backbone from said second data base; (5) identifying        amino acid residue side chains present in each sampled        segment; (6) determining the binding affinity value for all side        chains present in each sampled segment; and repeating steps (1)        through (5) for each said model and each said backbone;    -   a 13mer T-cell epitope peptide having a potential MHC class II        binding activity and created from non-modified INFβ, selected        from the group as depicted in FIG. 1 and its use for the        manufacture of INFβ having substantially no or less        immunogenicity than any non-modified molecule with the same        biological activity when used in vivo;    -   a peptide sequence consisting of at least 9 consecutive amino        acid residues of a 13mer T-cell epitope peptide as specified        above and its use for the manufacture of INFβ having        substantially no or less immunogenicity than any non-modified        molecule and having the biological activity of a human        interferon β when used in vivo;    -   a 13mer T-cell epitope peptide having a potential MHC class II        binding activity and created from non-modified INFβ, selected        from any of the group of sequences (a) or (b) as defined above        and its use for the manufacture of INFβ having substantially no        or less immunogenicity than any non-modified molecule and having        the biological activity of a human interferon β when used in        vivo;    -   a peptide sequence consisting of at least 9 consecutive amino        acid residues of a 13mer T-cell epitope peptide as derived from        any of the sequences (a) or (b) as specified above, and its use        for the manufacture of INFβ having substantially no or less        immunogenicity than any non-modified molecule and having the        biological activity of a human interferon β when used in vivo.

The term “T-cell epitope” means according to the understanding of thisinvention an amino acid sequence which is able to bind MHC class II,able to stimulate T-cells and/or also to bind (without necessarilymeasurably activating) T-cells in complex with MHC class II. The term“peptide” as used herein and in the appended claims, is a compound thatincludes two or more amino acids. The amino acids are linked together bya peptide bond (defined herein below). There are 20 different naturallyoccurring amino acids involved in the biological production of peptides,and any number of them may be linked in any order to form a peptidechain or ring. The naturally occurring amino acids employed in thebiological production of peptides all have the L-configuration.Synthetic peptides can be prepared employing conventional syntheticmethods, utilizing L-amino acids, D-amino acids, or various combinationsof amino acids of the two different configurations. Some peptidescontain only a few amino acid units. Short peptides, e.g., having lessthan ten amino acid units, are sometimes referred to as “oligopeptides”.Other peptides contain a large number of amino acid residues, e.g. up to100 or more, and are referred to as “polypeptides”. By convention, a“polypeptide” may be considered as any peptide chain containing three ormore amino acids, whereas a “oligopeptide” is usually considered as aparticular type of “short” polypeptide. Thus, as used herein, it isunderstood that any reference to a “polypeptide” also includes anoligopeptide. Further, any reference to a “peptide” includespolypeptides, oligopeptides, and proteins. Each different arrangement ofamino acids forms different polypeptides or proteins. The number ofpolypeptides—and hence the number of different proteins—that can beformed is practically unlimited.

“Alpha carbon (Cα)” is the carbon atom of the carbon-hydrogen (CH)component that is in the peptide chain. A “side chain” is a pendantgroup to Cα that can comprise a simple or complex group or moiety,having physical dimensions that can vary significantly compared to thedimensions of the peptide.

The invention may be applied to any INFβ species of molecule withsubstantially the same primary amino acid sequences as those disclosedherein and would include therefore INFβ molecules derived by geneticengineering means or other processes and may contain more or less than166 amino acid residues.

INFβ proteins such as identified from other mammalian sources have incommon many of the peptide sequences of the present disclosure and havein common many peptide sequences with substantially the same sequence asthose of the disclosed listing. Such protein sequences equally thereforefall under the scope of the present invention.

The invention is conceived to overcome the practical reality thatsoluble proteins introduced into autologous organisms can trigger animmune response resulting in development of host antibodies that bind tothe soluble protein. A prominent example of this phenomenon amongstothers, is the clinical use of interferon alpha 2 (INFα2). A significantproportion of human patients treated with INFα2 make antibodies despitethe fact that this protein is produced endogenously [Russo, D. et al(1996) ibid; Stein, R. et al (1988) ibid]. It is known that the clinicaluse of INFβ has also resulted in the development of immune responses tothe INFβ despite the fact that a molecule of at least identical primarystructure is produced endogenously in man [Kivisakk, P. et al (2000)Eur. J. Neurol. 7: 27-34; Myhr, K. M. et al (2000) Neurology 55:1569-1572]. The present invention seeks to address this by providingINFβ proteins with altered propensity to elicit an immune response onadministration to the human host. According to the methods describedherein, the inventors have discovered and now disclose the regions ofthe INFβ molecule comprising the critical T-cell epitopes driving theimmune responses to this autologous protein.

The general method of the present invention leading to the modified INFβcomprises the following steps:

-   (a) determining the amino acid sequence of the polypeptide or part    thereof;-   (b) identifying one or more potential T-cell epitopes within the    amino acid sequence of the protein by any method including    determination of the binding of the peptides to MHC molecules using    in vitro or in silico techniques or biological assays;-   (c) designing new sequence variants with one or more amino acids    within the identified potential T-cell epitopes modified in such a    way to substantially reduce or eliminate the activity of the T-cell    epitope as determined by the binding of the peptides to MHC    molecules using in vitro or in silico techniques or biological    assays. Such sequence variants are created in such a way to avoid    creation of new potential T-cell epitopes by the sequence variations    unless such new potential T-cell epitopes are, in turn, modified in    such a way to substantially reduce or eliminate the activity of the    T-cell epitope; and-   (d) constructing such sequence variants by recombinant DNA    techniques and testing said variants in order to identify one or    more variants with desirable properties according to well known    recombinant techniques.

The identification of potential T-cell epitopes according to step (b)can be carried out according to methods describes previously in theprior art. Suitable methods are disclosed in WO 98/59244; WO 98/52976;WO 00/34317 and may preferably be used to identify binding propensity ofINFβ-derived peptides to an MHC class II molecule.

Another very efficacious method for identifying T-cell epitopes bycalculation is described in the EXAMPLE 1 which is a preferredembodiment according to this invention.

In practice a number of variant INFβ proteins will be produced andtested for the desired immune and functional characteristic. The variantproteins will most preferably be produced by recombinant DNA techniquesalthough other procedures including chemical synthesis of INFβ fragmentsmay be contemplated. Chemical synthesis is for example particularlypreferred for the production of short INFβ fragments such as the R1 orR2 sequence elements disclosed herein and which comprise a particularembodiment of the present invention.

The results of an analysis according to step (b) of the above scheme andpertaining to the human INFβ protein sequence of 166 amino acid residuesis presented in FIG. 1. The results of a design and constructs accordingto step (c) and (d) of the above scheme and pertaining to the modifiedmolecule of this invention is presented in FIGS. 2 and 3.

The invention relates to INFβ analogues in which substitutions of atleast one amino acid residue have been made at positions resulting in asubstantial reduction in activity of or elimination of one or morepotential T-cell epitopes from the protein. One or more amino acidsubstitutions at particular points within any of the potential MHC classII ligands identified in FIG. 1 may result in a INFβ molecule with areduced immunogenic potential when administered as a therapeutic to thehuman host.

It is most preferred to provide an INFβ molecule in which amino acidmodification (e.g. a substitution) is conducted within the mostimmunogenic regions of the parent molecule. The inventors herein havediscovered that the most immunogenic regions of the INFβ molecule in manare confined to two regions R1and R2 comprising respectively amino acidsequences; QFQKEDAALTIYEMLQNIFAIFRQ (SEQ ID NO: 2) andRYYGRILHYLKAKEYSHCAWT (SEQ ID NO: 3). respectively. The major preferredembodiments of the present invention comprise INFβ molecules for whichthe MHC class II ligands of FIG. 1 and which align either in theirentirety or to a minimum of 9 amino acid residues with any of the abovesequence elements R1 or R2 are altered such as to eliminate binding orotherwise reduce the numbers of MHC allotypes to which the peptide canbind.

The preferred embodiments of the invention include the specificsubstitutions of FIG. 4. It is particularly preferred to providemodified INFβ molecules containing combinations of substitutions fromFIG. 4. Combinations which comprise multiple (greater than 1)modification both within each of the immunogenic regions R1 and R2, andcombinations comprising multiple modifications to both R1 and R2 withinthe same molecule are especially preferred although such preference isnot intended to limit the combinations of substitution which areconsidered desirable.

For the elimination of T-cell epitopes, amino acid substitutions arepreferably made at appropriate points within the peptide sequencepredicted to achieve substantial reduction or elimination of theactivity of the T-cell epitope. In practice an appropriate point willpreferably equate to an amino acid residue binding within one of thepockets provided within the MHC class II binding groove.

It is most preferred to alter binding within the first pocket of thecleft at the so-called P1 or P1 anchor position of the peptide. Thequality of binding interaction between the P1 anchor residue of thepeptide and the first pocket of the MHC class II binding groove isrecognized as being a major determinant of overall binding affinity forthe whole peptide. An appropriate substitution at this position of thepeptide will be for a residue less readily accommodated within thepocket, for example, substitution to a more hydrophilic residue. Aminoacid residues in the peptide at positions equating to binding withinother pocket regions within the MHC binding cleft are also consideredand fall under the scope of the present.

It is understood that single amino acid substitutions within a givenpotential T-cell epitope are the most preferred route by which theepitope may be eliminated. Combinations of substitution within a singleepitope may be contemplated and for example can be particularlyappropriate where individually defined epitopes are in overlap with eachother. Moreover, amino acid substitutions either singly within a givenepitope or in combination within a single epitope may be made atpositions not equating to the “pocket residues” with respect to the MHCclass II binding groove, but at any point within the peptide sequence.Substitutions may be made with reference to an homologues structure orstructural method produced using in silico techniques known in the artand may be based on known structural features of the molecule accordingto this invention. All such substitutions fall within the scope of thepresent invention.

Amino acid substitutions other than within the peptides identified abovemay be contemplated particularly when made in combination withsubstitution(s) made within a listed peptide. For example a change maybe contemplated to restore structure or biological activity of thevariant molecule. Such compensatory changes and changes to includedeletion or addition of particular amino acid residues from the INFβpolypeptide resulting in a variant with desired activity and incombination with changes in any of the disclosed peptides fall under thescope of the present.

In as far as this invention relates to modified INFβ, compositionscontaining such modified INFβ proteins or fragments of modified INFβproteins and related compositions should be considered within the scopeof the invention. In another aspect, the present invention relates tonucleic acids encoding modified INFβ entities. In a further aspect thepresent invention relates to methods for therapeutic treatment of humansusing the modified INFβ proteins. In a further aspect still, theinvention relates to methods for therapeutic treatment usingpharmaceutical preparations comprising peptide or derivative moleculeswith sequence identity or part identity with the sequences hereindisclosed as R1 or R2.

The invention will now be illustrated, but not limited, by the followingexamples. The examples refer to the following drawings:

FIG. 1 provides a table of peptide sequences in human INFβ withpotential human MHC class II binding activity. Peptides are 13mers,amino acids are identified using single letter code

FIG. 2 provides a table detailing amino acid substitutions leading tothe elimination of T-cell epitopes of human INFβ. WT=wild type residue.

FIG. 3 provides a table detailing additional substitutions leading tothe removal of a potential T-cell epitope for 1 or more MHC allotypes.

FIG. 4 provides a table of preferred substitutions in human INFβ.WT=wild type residue; #=position; MUT=desired residue. The tableindicates the epitope region (R1 or R2) in which each substitution islocated.

FIG. 5 provides a table of the INFβ 15-mer peptide sequences analyzedusing the naïve human in vitro T-cell assay of EXAMPLE 2. The peptideID#, SEQ ID NO, and position of the N-terminal peptide residue of eachpotential epitope sequence within the INFβ sequence is indicated.

FIG. 6 shows cumulative stimulation indexes from 6 individuals thatrespond to stimulation with IFNβ peptides. Panel 6a shows resultsfollowing stimulation using peptides at 1 μM concentration. Panel 6bshows results following stimulation using peptides at 10 μMconcentration. Six donors from 20 screened responded to stimulation withone or more peptides from the IFNβ sequence. Responses to individualpeptides are grouped into two distinct regions R1 and R2. Controlpeptides C32 (DRB 1-restricted) and C49 (DP-restricted) are included forcomparison. Cross-hatching within each bar indicates the contributionfrom individual donors. SI=stimulation index.

FIG. 7 shows the donor specific stimulation responses to the INFβsynthetic peptides. Panels 7a-7f show individual donor responses topeptides at 1 μM (light bars) and 10 μM (dark bars) final peptideconcentration. Data from control peptides C32 (DRB1-restricted) and C49(DP-restricted) are included in each panel for comparison. Threshold forpositive stimulation index=2.

FIG. 8 shows the immunogenic regions within INFβ and details the peptidesequences from these regions able to stimulate naïve human T-cells.

FIG. 9 provides a table indicating INFβ peptides capable of promotingproliferation of naïve human T-cells in vitro. For two of the donors,responses are recorded to multiple overlapping peptides from eitherepitope region R1 or R2. Responses to individual synthetic peptidesmapping to epitope regions R1 or R2 are scored from six donors.

FIG. 10 provides representative data of the anti-ptoliferative effect oftwo modified INFβ molecules. Assays were conducted according to themethods of EXAMPLE 4. In each of panels a) and b), antiproliferativeeffects of control treatments are recorded Controls comprisenon-modified INFβ-Fc fusion=WT-FcINFb; a standard INFβ preparation=R&DIFNb and media containing no INF=Media Con. Panel a) shows data for Leu57 Ala (IFNβ-BIOV7) modified INFβ. Panel b) shows data for the Phe 67His (IFNβ-BIOV12) modified INFβ.

EXAMPLE 1

There are a number of factors that play important roles in determiningthe total structure of a protein or polypeptide. First, the peptidebond, i.e., that bond which joins the amino acids in the chain together,is a covalent bond. This bond is planar in structure, essentially asubstituted amide. An “amide” is any of a group of organic compoundscontaining the grouping —CONH—.

The planar peptide bond linking Cα of adjacent amino acids may berepresented as depicted below:

Because the O═C and the C—N atoms lie in a relatively rigid plane, freerotation does not occur about these axes. Hence, a plane schematicallydepicted by the interrupted line is sometimes referred to as an “amide”or “peptide plane” plane wherein lie the oxygen (O), carbon (C),nitrogen (N), and hydrogen (H) atoms of the peptide backbone. Atopposite corners of this amide plane are located the Cα atoms. Sincethere is substantially no rotation about the O═C and C—N atoms in thepeptide or amide plane, a polypeptide chain thus comprises a series ofplanar peptide linkages joining the Cα atoms.

A second factor that plays an important role in defining the totalstructure or conformation of a polypeptide or protein is the angle ofrotation of each amide plane about the common Cα linkage. The terms“angle of rotation” and “torsion angle” are hereinafter regarded asequivalent terms. Assuming that the O, C, N, and H atoms remain in theamide plane (which is usually a valid assumption, although there may besome slight deviations from planarity of these atoms for someconformations), these angles of rotation define the N and Rpolypeptide's backbone conformation, i.e., the structure as it existsbetween adjacent residues. These two angles are known as φ and ψ. A setof the angles φ_(i), ψ_(i) where the subscript i represents a particularresidue of a polypeptide chain, thus effectively defines the polypeptidesecondary structure. The conventions used in defining the φ, ψ angles,i.e., the reference points at which the amide planes form a zero degreeangle, and the definition of which angle is φ, and which angle is ψ, fora given polypeptide, are defined in the literature. See, e.g,Ramachandran et al. Adv. Prot. Chem. 23:283-437 (1968), at pages 285-94,which pages are incorporated herein by reference.

The present method can be applied to any protein, and is based in partupon the discovery that in humans the primary Pocket 1 anchor positionof MHC Class II molecule binding grooves has a well designed specificityfor particular amino acid side chains. The specificity of this pocket isdetermined by the identity of the amino acid at position 86 of the betachain of the MHC Class II molecule. This site is located at the bottomof Pocket 1 and determines the size of the side chain that can beaccommodated by this pocket. Marshall, K. W., J. Immunol., 152:4946-4956(1994). If this residue is a glycine, then all hydrophobic aliphatic andaromatic amino acids (hydrophobic aliphatics being: valine, leucine,isoleucine, methionine and aromatics being: phenylalanine, tyrosine andtryptophan) can be accommodated in the pocket, a preference being forthe aromatic side chains. If this pocket residue is a valine, then theside chain of this amino acid protrudes into the pocket and restrictsthe size of peptide side chains that can be accommodated such that onlyhydrophobic aliphatic side chains can be accommodated. Therefore, in anamino acid residue sequence, wherever an amino acid with a hydrophobicaliphatic or aromatic side chain is found, there is the potential for aMHC Class II restricted T-cell epitope to be present. If the side-chainis hydrophobic aliphatic, however, it is approximately twice as likelyto be associated with a T-cell epitope than an aromatic side chain(assuming an approximately even distribution of Pocket 1 typesthroughout the global population).

A computational method embodying the present invention profiles thelikelihood of peptide regions to contain T-cell epitopes as follows:

(1) The primary sequence of a peptide segment of predetermined length isscanned, and all hydrophobic aliphatic and aromatic side chains presentare identified. (2) The hydrophobic aliphatic side chains are assigned avalue greater than that for the aromatic side chains; preferably abouttwice the value assigned to the aromatic side chains, e.g., a value of 2for a hydrophobic aliphatic side chain and a value of 1 for an aromaticside chain. (3) The values determined to be present are summed for eachoverlapping amino acid residue segment (window) of predetermined uniformlength within the peptide, and the total value for a particular segment(window) is assigned to a single amino acid residue at an intermediateposition of the segment (window), preferably to a residue at about themidpoint of the sampled segment (window). This procedure is repeated foreach sampled overlapping amino acid residue segment (window). Thus, eachamino acid residue of the peptide is assigned a value that relates tothe likelihood of a T-cell epitope being present in that particularsegment (window). (4) The values calculated and assigned as described inStep 3, above, can be plotted against the amino acid coordinates of theentire amino acid residue sequence being assessed. (5) All portions ofthe sequence which have a score of a predetermined value, e.g., a valueof 1, are deemed likely to contain a T-cell epitope and can be modified,if desired.

This particular aspect of the present invention provides a generalmethod by which the regions of peptides likely to contain T-cellepitopes can be described. Modifications to the peptide in these regionshave the potential to modify the MHC Class II binding characteristics.

According to another aspect of the present invention, T-cell epitopescan be predicted with greater accuracy by the use of a moresophisticated computational method which takes into account theinteractions of peptides with models of MHC Class II alleles.

The computational prediction of T-cell epitopes present within a peptideaccording to this particular aspect contemplates the construction ofmodels of at least 42 MHC Class II alleles based upon the structures ofall known MHC Class II molecules and a method for the use of thesemodels in the computational identification of T-cell epitopes, theconstruction of libraries of peptide backbones for each model in orderto allow for the known variability in relative peptide backbone alphacarbon (Cα) positions, the construction of libraries of amino-acid sidechain conformations for each backbone dock with each model for each ofthe 20 amino-acid alternatives at positions critical for the interactionbetween peptide and MHC Class II molecule, and the use of theselibraries of backbones and side-chain conformations in conjunction witha scoring function to select the optimum backbone and side-chainconformation for a particular peptide docked with a particular MHC ClassII molecule and the derivation of a binding score from this interaction.

Models of MHC Class II molecules can be derived via homology modelingfrom a number of similar structures found in the Brookhaven Protein DataBank (“PDB”). These may be made by the use of semi-automatic homologymodeling software (Modeller, Sali A. & Blundell T L., 1993. J. Mol Biol234:779-815) which incorporates a simulated annealing function, inconjunction with the CHARMm force-field for energy minimisation(available from Molecular Simulations Inc., San Diego, Calif.).Alternative modeling methods can be utilized as well.

The present method differs significantly from other computationalmethods which use libraries of experimentally derived binding data ofeach amino-acid alternative at each position in the binding groove for asmall set of MHC Class II molecules (Marshall, K. W., et al., Biomed.Pept. Proteins Nucleic Acids, 1(3):157-162) (1995) or yet othercomputational methods which use similar experimental binding data inorder to define the binding characteristics of particular types ofbinding pockets within the groove, again using a relatively small subsetof MHC Class II molecules, and then ‘mixing and matching’ pocket typesfrom this pocket library to artificially create further ‘virtual’ MHCClass II molecules (Sturniolo T., et al., Nat. Biotech,17(6): 555-561(1999). Both prior methods suffer the major disadvantage that, due tothe complexity of the assays and the need to synthesize large numbers ofpeptide variants, only a small number of MHC Class II molecules can beexperimentally scanned. Therefore the first prior method can only makepredictions for a small number of MHC Class II molecules. The secondprior method also makes the assumption that a pocket lined with similaramino-acids in one molecule will have the same binding characteristicswhen in the context of a different Class II allele and suffers furtherdisadvantages in that only those MHC Class II molecules can be‘virtually’ created which contain pockets contained within the pocketlibrary. Using the modeling approach described herein, the structure ofany number and type of MHC Class II molecules can be deduced, thereforealleles can be specifically selected to be representative of the globalpopulation. In addition, the number of MHC Class II molecules scannedcan be increased by making further models further than having togenerate additional data via complex experimentation.

The use of a backbone library allows for variation in the positions ofthe Cα atoms of the various peptides being scanned when docked withparticular MHC Class II molecules. This is again in contrast to thealternative prior computational methods described above which rely onthe use of simplified peptide backbones for scanning amino-acid bindingin particular pockets. These simplified backbones are not likely to berepresentative of backbone conformations found in ‘real’ peptidesleading to inaccuracies in prediction of peptide binding. The presentbackbone library is created by superposing the backbones of all peptidesbound to MHC Class II molecules found within the Protein Data Bank andnoting the root mean square (RMS) deviation between the Cα atoms of eachof the eleven amino-acids located within the binding groove. While thislibrary can be derived from a small number of suitable available mouseand human structures (currently 13), in order to allow for thepossibility of even greater variability, the RMS figure for each C″-αposition is increased by 50%. The average Cα position of each amino-acidis then determined and a sphere drawn around this point whose radiusequals the RMS deviation at that position plus 50%. This sphererepresents all allowed Cα positions.

Working from the Cα with the least RMS deviation (that of the amino-acidin Pocket 1 as mentioned above, equivalent to Position 2 of the 11residues in the binding groove), the sphere is three-dimensionallygridded, and each vertex within the grid is then used as a possiblelocation for a Cα of that amino-acid. The subsequent amide plane,corresponding to the peptide bond to the subsequent amino-acid isgrafted onto each of these Cαs and the φ and ψ angles are rotatedstep-wise at set intervals in order to position the subsequent Cα. Ifthe subsequent Cα falls within the ‘sphere of allowed positions’ forthis Cα than the orientation of the dipeptide is accepted, whereas if itfalls outside the sphere then the dipeptide is rejected. This process isthen repeated for each of the subsequent Cα positions, such that thepeptide grows from the Pocket 1 Cα ‘seed’, until all nine subsequent Cαshave been positioned from all possible permutations of the precedingCαs. The process is then repeated once more for the single Cα precedingpocket 1 to create a library of backbone Cα positions located within thebinding groove.

The number of backbones generated is dependent upon several factors: Thesize of the ‘spheres of allowed positions’; the fineness of the griddingof the ‘primary sphere’ at the Pocket 1 position; the fineness of thestep-wise rotation of the φ and ψ angles used to position subsequentCαs. Using this process, a large library of backbones can be created.The larger the backbone library, the more likely it will be that theoptimum fit will be found for a particular peptide within the bindinggroove of an MHC Class II molecule. Inasmuch as all backbones will notbe suitable for docking with all the models of MHC Class II moleculesdue to clashes with amino-acids of the binding domains, for each allelea subset of the library is created comprising backbones which can beaccommodated by that allele.

The use of the backbone library, in conjunction with the models of MHCClass II molecules creates an exhaustive database consisting of allowedside chain conformations for each amino-acid in each position of thebinding groove for each MHC Class II molecule docked with each allowedbackbone. This data set is generated using a simple steric overlapfunction where a MHC Class II molecule is docked with a backbone and anamino-acid side chain is grafted onto the backbone at the desiredposition. Each of the rotatable bonds of the side chain is rotatedstep-wise at set intervals and the resultant positions of the atomsdependent upon that bond noted. The interaction of the atom with atomsof side-chains of the binding groove is noted and positions are eitheraccepted or rejected according to the following criteria: The sum totalof the overlap of all atoms so far positioned must not exceed apre-determined value.

Thus the stringency of the conformational search is a function of theinterval used in the step-wise rotation of the bond and thepre-determined limit for the total overlap. This latter value can besmall if it is known that a particular pocket is rigid, however thestringency can be relaxed if the positions of pocket side-chains areknown to be relatively flexible. Thus allowances can be made to imitatevariations in flexibility within pockets of the binding groove. Thisconformational search is then repeated for every amino-acid at everyposition of each backbone when docked with each of the MHC Class IImolecules to create the exhaustive database of side-chain conformations.

A suitable mathematical expression is used to estimate the energy ofbinding between models of MHC Class II molecules in conjunction withpeptide ligand conformations which have to be empirically derived byscanning the large database of backbone/side-chain conformationsdescribed above. Thus a protein is scanned for potential T-cell epitopesby subjecting each possible peptide of length varying between 9 and 20amino-acids (although the length is kept constant for each scan) to thefollowing computations: An MHC Class II molecule is selected togetherwith a peptide backbone allowed for that molecule and the side-chainscorresponding to the desired peptide sequence are grafted on. Atomidentity and interatomic distance data relating to a particularside-chain at a particular position on the backbone are collected foreach allowed conformation of that amino-acid (obtained from the databasedescribed above). This is repeated for each side-chain along thebackbone and peptide scores derived using a scoring function. The bestscore for that backbone is retained and the process repeated for eachallowed backbone for the selected model. The scores from all allowedbackbones are compared and the highest score is deemed to be the peptidescore for the desired peptide in that MHC Class II model. This processis then repeated for each model with every possible peptide derived fromthe protein being scanned, and the scores for peptides versus models aredisplayed.

In the context of the present invention, each ligand presented for thebinding affinity calculation is an amino-acid segment selected from apeptide or protein as discussed above. Thus, the ligand is a selectedstretch of amino acids about 9 to 20 amino acids in length derived froma peptide, polypeptide or protein of known sequence. The terms “aminoacids” and “residues” are hereinafter regarded as equivalent terms.

The ligand, in the form of the consecutive amino acids of the peptide tobe examined grafted onto a backbone from the backbone library, ispositioned in the binding cleft of an MHC Class II molecule from the MHCClass II molecule model library via the coordinates of the C″-α atoms ofthe peptide backbone and an allowed conformation for each side-chain isselected from the database of allowed conformations. The relevant atomidentities and interatomic distances are also retrieved from thisdatabase and used to calculate the peptide binding score. Ligands with ahigh binding affinity for the MHC Class II binding pocket are flagged ascandidates for site-directed mutagenesis. Amino-acid substitutions aremade in the flagged ligand (and hence in the protein of interest) whichis then retested using the scoring function in order to determinechanges which reduce the binding affinity below a predeterminedthreshold value. These changes can then be incorporated into the proteinof interest to remove T-cell epitopes.

Binding between the peptide ligand and the binding groove of MHC ClassII molecules involves non-covalent interactions including, but notlimited to: hydrogen bonds, electrostatic interactions, hydrophobic(lipophilic) interactions and Van der Walls interactions. These areincluded in the peptide scoring function as described in detail below.

It should be understood that a hydrogen bond is a non-covalent bondwhich can be formed between polar or charged groups and consists of ahydrogen atom shared by two other atoms. The hydrogen of the hydrogendonor has a positive charge where the hydrogen acceptor has a partialnegative charge. For the purposes of peptide/protein interactions,hydrogen bond donors may be either nitrogens with hydrogen attached orhydrogens attached to oxygen or nitrogen. Hydrogen bond acceptor atomsmay be oxygens not attached to hydrogen, nitrogens with no hydrogensattached and one or two connections, or sulphurs with only oneconnection. Certain atoms, such as oxygens attached to hydrogens orimine nitrogens (e.g. C═NH) may be both hydrogen acceptors or donors.Hydrogen bond energies range from 3 to 7 Kcal/mol and are much strongerthan Van der Waal's bonds, but weaker than covalent bonds. Hydrogenbonds are also highly directional and are at their strongest when thedonor atom, hydrogen atom and acceptor atom are co-linear.

Electrostatic bonds are formed between oppositely charged ion pairs andthe strength of the interaction is inversely proportional to the squareof the distance between the atoms according to Coulomb's law. Theoptimal distance between ion pairs is about 2.8 Å. In protein/peptideinteractions, electrostatic bonds may be formed between arginine,histidine or lysine and aspartate or glutamate. The strength of the bondwill depend upon the pKa of the ionizing group and the dielectricconstant of the medium although they are approximately similar instrength to hydrogen bonds.

Lipophilic interactions are favorable hydrophobic-hydrophobic contactsthat occur between he protein and peptide ligand. Usually, these willoccur between hydrophobic amino acid side chains of the peptide buriedwithin the pockets of the binding groove such that they are not exposedto solvent. Exposure of the hydrophobic residues to solvent is highlyunfavorable since the surrounding solvent molecules are forced tohydrogen bond with each other forming cage-like clathrate structures.The resultant decrease in entropy is highly unfavorable. Lipophilicatoms may be sulphurs which are neither polar nor hydrogen acceptors andcarbon atoms which are not polar.

Van der Waal's bonds are non-specific forces found between atoms whichare 3-4 Å apart. They are weaker and less specific than hydrogen andelectrostatic bonds. The distribution of electronic charge around anatom changes with time and, at any instant, the charge distribution isnot symmetric. This transient asymmetry in electronic charge induces asimilar asymmetry in neighboring atoms. The resultant attractive forcesbetween atoms reaches a maximum at the Van der Waal's contact distancebut diminishes very rapidly at about 1 Å to about 2 Å. Conversely, asatoms become separated by less than the contact distance, increasinglystrong repulsive forces become dominant as the outer electron clouds ofthe atoms overlap. Although the attractive forces are relatively weakcompared to electrostatic and hydrogen bonds (about 0.6 Kcal/mol), therepulsive forces in particular may be very important in determiningwhether a peptide ligand may bind successfully to a protein.

In one embodiment, the Böhm scoring function (SCORE1 approach) is usedto estimate the binding constant. (Böhm, H. J., J Comput Aided Mol.Des., 8(3):243-256 (1994) which is hereby incorporated in its entirety).In another embodiment, the scoring function (SCORE2 approach) is used toestimate the binding affinities as an indicator of a ligand containing aT-cell epitope (Böhm, H. J., J. Comput Aided Mol. Des., 12(4):309-323(1998) which is hereby incorporated in its entirety). However, the Böhmscoring functions as described in the above references are used toestimate the binding affinity of a ligand to a protein where it isalready known that the ligand successfully binds to the protein and theprotein/ligand complex has had its structure solved, the solvedstructure being present in the Protein Data Bank (“PDB”). Therefore, thescoring function has been developed with the benefit of known positivebinding data. In order to allow for discrimination between positive andnegative binders, a repulsion term must be added to the equation. Inaddition, a more satisfactory estimate of binding energy is achieved bycomputing the lipophilic interactions in a pairwise manner rather thanusing the area based energy term of the above Böhm functions.

Therefore, in a preferred embodiment, the binding energy is estimatedusing a modified Böhm scoring function. In the modified Böhm scoringfunction, the binding energy between protein and ligand (ΔG_(bind)) isestimated considering the following parameters: The reduction of bindingenergy due to the overall loss of translational and rotational entropyof the ligand (ΔG₀); contributions from ideal hydrogen bonds (ΔG_(hb))where at least one partner is neutral; contributions from unperturbedionic interactions (ΔG_(ionic)); lipophilic interactions betweenlipophilic ligand atoms and lipophilic acceptor atoms (ΔG_(lipo)); theloss of binding energy due to the freezing of internal degrees offreedom in the ligand, i.e., the freedom of rotation about each C—C bondis reduced (ΔG_(rot)); the energy of the interaction between the proteinand ligand (E_(VdW)). Consideration of these terms gives equation 1:(ΔG _(bind))=(ΔG ₀)+(ΔG _(hb) ×N _(hb))+(ΔG _(ionic) ×N _(ionic))+(ΔG_(lipo) ×N _(lipo))+×N _(lipo))+(ΔG _(rot) +N _(rot))+(E _(VdW)).

Where N is the number of qualifying interactions for a specific termand, in one embodiment, ΔG₀, ΔG_(hb), ΔG_(ionic), ΔG_(lipo) and ΔG_(rot)are constants which are given the values: 5.4, −4.7, −4.7, −0.17, and1.4, respectively.

The term N_(hb) is calculated according to equation 2:N _(hb)=Σ_(h-bonds) f(ΔR, Δα)×f(N _(neighb))×f _(pcs)f(ΔR, Δα) is a penalty function which accounts for large deviations ofhydrogen bonds from ideality and is calculated according to equation 3:f(ΔR, Δ−α)=f1 (ΔR)×f2(Δα)Where:

f1((R)=1 if (R<=TOL

or =1−((R−TOL)/0.4 if (R<=0.4+TOL

or =0 if (R>0.4+TOL

And:

f2((( )=1 if ((<30°

or =1−(Δα−30)/50 if Δα<=80°

or =0 if Δα>80°

-   TOL is the tolerated deviation in hydrogen bond length=0.25Å-   ΔR is the deviation of the H—O/N hydrogen bond length from the ideal    value=1.9 Å-   Δα is the deviation of the hydrogen bond angle ∠_(N/O-H . . . O/N)    from its idealized value of 180° f(N_(neighb)) distinguishes between    concave and convex parts of a protein surface and therefore assigns    greater weight to polar interactions found in pockets rather than    those found at the protein surface. This function is calculated    according to equation 4 below:    f(N _(neighb))=(N _(neighb) /N _(neighb,0))^(α) where α=0.5    N_(neighb) is the number of non-hydrogen protein atoms that are    closer than 5 Å to any given protein atom.    N_(neighb,0) is a constant=25

f_(pcs) is a function which allows for the polar contact surface areaper hydrogen bond and therefore distinguishes between strong and weakhydrogen bonds and its value is determined according to the followingcriteria:

-   f_(pcs)=β when A_(polar)/N_(HB)<10 Å²-   or f_(pcs)=l when A_(polar)/N_(HB)<10 Å²-   A_(polar) is the size of the polar protein-ligand contact surface-   N_(HB) is the number of hydrogen bonds-   β is a constant whose value=1.2

For the implementation of the modified Böhm scoring function, thecontributions from ionic interactions, ΔG_(ionic), are computed in asimilar fashion to those from hydrogen bonds described above since thesame geometry dependency is assumed.

The term N_(lipo) is calculated according to equation 5 below:N _(lipo) =Σ _(lL) f(r _(lL))

f(r_(lL)) is calculated for all lipophilic ligand atoms, l, and alllipophilic protein atoms, L, according to the following criteria:

-   f(r_(lL))=1 when r_(lL)<=R1f(rlL)=(r_(lL)−R1)/(R2−R1) when R2<r-   f (r_(lL))=0 when r_(lL)>=R2-   Where: R1=r_(l) ^(vdw)+r_(L) ^(vdw)+0.5-   and R2=R1+3.0-   and r_(l) ^(vdw) is the Van der Waal's radius of atom l-   and r_(L) ^(vdw) is the Van der Waal's radius of atom L

The term N_(rot) is the number of rotable bonds of the amino acid sidechain and is taken to be the number of acyclic sp³-sp³ and sp³-sp²bonds. Rotations of terminal —CH₃ or —NH₃ are not taken into account.

The final term, E_(VdW), is calculated according to equation 6 below:E _(VdW)=ε₁ε₂((r ₁ ^(vdw) +r ₂ ^(vdw))¹² /r ¹²−(r ₁ ^(vdw) +r ₂ ^(vdw))⁶/r ⁶), where;

-   ε₁ and ε₂ are constants dependant upon atom identity-   r₁ ^(vdw)+r₂ ^(vdw) are the Van der Waal's atomic radii-   r is the distance between a pair of atoms.

With regard to Equation 6, in one embodiment, the constants ε₁ and ε₂are given the atom values: C: 0.245, N: 0.283, O: 0.316, S: 0.316,respectively (i.e. for atoms of Carbon, Nitrogen, Oxygen and Sulphur,respectively). With regards to equations 5 and 6, the Van der Waal'sradii are given the atom values C: 1.85, N: 1.75, O: 1.60, S: 2.00 Å.

It should be understood that all predetermined values and constantsgiven in the equations above are determined within the constraints ofcurrent understandings of protein ligand interactions with particularregard to the type of computation being undertaken herein. Therefore, itis possible that, as this scoring function is refined further, thesevalues and constants may change hence any suitable numerical value whichgives the desired results in terms of estimating the binding energy of aprotein to a ligand may be used and hence fall within the scope of thepresent invention.

As described above, the scoring function is applied to data extractedfrom the database of side-chain conformations, atom identities, andinteratomic distances. For the purposes of the present description, thenumber of MHC Class II molecules included in this database is 42 modelsplus four solved structures. It should be apparent from the abovedescriptions that the modular nature of the construction of thecomputational method of the present invention means that new models cansimply be added and scanned with the peptide backbone library andside-chain conformational search function to create additional data setswhich can be processed by the peptide scoring function as describedabove. This allows for the repertoire of scanned MHC Class II moleculesto easily be increased, or structures and associated data to be replacedif data are available to create more accurate models of the existingalleles.

The present prediction method can be calibrated against a data setcomprising a large number of peptides whose affinity for various MHCClass II molecules has previously been experimentally determined. Bycomparison of calculated versus experimental data, a cut of value can bedetermined above which it is known that all experimentally determinedT-cell epitopes are correctly predicted.

It should be understood that, although the above scoring function isrelatively simple compared to some sophisticated methodologies that areavailable, the calculations are performed extremely rapidly. It shouldalso be understood that the objective is not to calculate the truebinding energy per se for each peptide docked in the binding groove of aselected MHC Class II protein. The underlying objective is to obtaincomparative binding energy data as an aid to predicting the location ofT-cell epitopes based on the primary structure (i.e. amino acidsequence) of a selected protein. A relatively high binding energy or abinding energy above a selected threshold value would suggest thepresence of a T-cell epitope in the ligand. The ligand may then besubjected to at least one round of amino-acid substitution and thebinding energy recalculated. Due to the rapid nature of thecalculations, these manipulations of the peptide sequence can beperformed interactively within the program's user interface oncost-effectively available computer hardware. Major investment incomputer hardware is thus not required.

It would be apparent to one skilled in the art that other availablesoftware could be used for the same purposes. In particular, moresophisticated software which is capable of docking ligands into proteinbinding-sites may be used in conjunction with energy minimization.Examples of docking software are: DOCK (Kuntz et al., J. Mol. Biol.,161:269-288 (1982)), LUDI (Böhm, H. J., J. Comput Aided Mol. Des.,8:623-632 (1994)) and FLEXX (Rarey M., et al., ISMB, 3:300-308 (1995)).Examples of molecular modeling and manipulation software include: AMBER(Tripos) and CHARMm (Molecular Simulations Inc.). The use of thesecomputational methods would severely limit the throughput of the methodof this invention due to the lengths of processing time required to makethe necessary calculations. However, it is feasible that such methodscould be used as a ‘secondary screen’ to obtain more accuratecalculations of binding energy for peptides which are found to be‘positive binders’ via the method of the present invention.

The limitation of processing time for sophisticated molecular mechanicor molecular dynamic calculations is one which is defined both by thedesign of the software which makes these calculations and the currenttechnology limitations of computer hardware. It may be anticipated that,in the future, with the writing of more efficient code and thecontinuing increases in speed of computer processors, it may becomefeasible to make such calculations within a more manageable time-frame.

Further information on energy functions applied to macromolecules andconsideration of the various interactions that take place within afolded protein structure can be found in: Brooks, B. R., et al., J.Comput. Chem., 4:187-217 (1983) and further information concerninggeneral protein-ligand interactions can be found in: Dauber-Osguthorpeet al., Proteins 4(1):31-47(1988), which are incorporated herein byreference in their entirety. Useful background information can also befound, for example, in Fasman, G. D., ed., Prediction of ProteinStructure and the Principles of Protein Conformation, Plenum Press, NewYork, ISBN: 0-306 4313-9.

EXAMPLE 2

The interaction between MHC, peptide and T-cell receptor (TCR) providesthe structural basis for the antigen specificity of T-cell recognition.T-cell proliferation assays test the binding of peptides to MHC and therecognition of MHC/peptide complexes by the TCR. In vitro T-cellproliferation assays of the present example, involve the stimulation ofperipheral blood mononuclear cells (PBMCs), containing antigenpresenting cells (APCs) and T-cells. Stimulation is conducted in vitrousing synthetic peptide antigens, and in some experiments whole proteinantigen. Stimulated T-cell proliferation is measured using ³H-thymidine(³H-Thy) and the presence of incorporated ³H-Thy assessed usingscintillation counting of washed fixed cells.

Buffy coats from human blood stored for less than 12 hours were obtainedfrom the National Blood Service (Addenbrooks Hospital, Cambridge, UK).Ficoll-paque was obtained from Amersham Pharmacia Biotech (Amersham,UK). Serum free AIM V media for the culture of primary human lymphocytesand containing L-glutamine, 50 μg/ml streptomycin, 10 μg/ml gentomycinand 0.1% human serum albumin was from Gibco-BRL (Paisley, UK). Syntheticpeptides were obtained from Eurosequence (Groningen, The Netherlands)and Babraham Technix (Cambridge, UK). Erythrocytes and leukocytes wereseparated from plasma and platelets by gentle centrifugation of buffycoats. The top phase (containing plasma and platelets) was removed anddiscarded. Erythrocytes and leukocytes were diluted 1:1 in phosphatebuffered saline (PBS) before layering onto 15 ml ficoll-paque (AmershamPharmacia, Amersham UK). Centrifugation was done according to themanufacturers recommended conditions and PBMCs were harvested from theserum+PBS/ficoll paque interface. PBMCs were mixed with PBS (1:1) andcollected by centrifugation. The supernatant was removed and discardedand the PBMC pellet resuspended in 50 ml PBS. Cells were again pelletedby centrifugation and the PBS supernatant discarded. Cells wereresuspended using 50 ml AIM V media and at this point counted andviability assessed using trypan blue dye exclusion. Cells were againcollected by centrifugation and the supernatant discarded. Cells wereresuspended for cryogenic storage at a density of 3×10⁷ per ml. Thestorage medium was 90%(v/v) heat inactivated AB human serum (Sigma,Poole, UK) and 10%(v/v) DMSO (Sigma, Poole, UK). Cells were transferredto a regulated freezing container (Sigma) and placed at −70° C.overnight. When required for use, cells were thawed rapidly in a waterbath at 37° C. before transferring to 10 ml pre-warmed AIM V medium.

PBMC were stimulated with protein and peptide antigens in a 96 well flatbottom plate at a density of 2×10⁵ PBMC per well. PBMC were incubatedfor 7 days at 37° C. before pulsing with ³H-Thy (Amersham-Phamacia,Amersham, UK). For the present study, synthetic peptides (15mers) thatoverlapped by 3aa increments were generated that spanned the entiresequence of IFNβ. Peptide identification numbers (ID#) and sequences aregiven in FIG. 5. Each peptide was screened individually against PBMC'sisolated from 20 naïve donors. Two control peptides that have previouslybeen shown to be immunogenic and a potent non-recall antigen KLH wereused in each donor assay.

The control antigens used in this study :are shown in Table 1.

Table 1. Control Antigens.

Peptide Sequence C-32 Biotin-PKYVKQNTLKLAT (SEQ ID NO: 6) Fluhaemagglutinin 307-319 C-49 KVVDQIKKISKPVQH (SEQ ID NO: 7) Chlamydia HSP60 peptide KLH Whole protein from Keyhole Limpet Hemocyanin.

Peptides were dissolved in DMSO to a final concentration of 10 mM, thesestock solutions were then diluted 1/500 in AIM V media (finalconcentration 20 μM). Peptides were added to a flat bottom 96 well plateto give a final concentration of 2 and 20 μM in a 100 μl. The viabilityof thawed PBMC's was assessed by trypan blue dye exclusion, cells werethen resuspended at a density of 2×10⁶ cells/ml, and 100 μl (2×10⁵PBMC/well) was transferred to each well containing peptides. Triplicatewell cultures were assayed at each peptide concentration. Plates wereincubated for 7 days in a humidified atmosphere of 5% CO₂ at 37° C.Cells were pulsed for 18-21 hours with 1 μCi ³H-Thy/well beforeharvesting onto filter mats. CPM values were determined using a Wallacmicroplate beta top plate counter (Perkin Elmer). Results were expressedas stimulation indices, determined using the following formula:

$\frac{{Proliferation}\mspace{14mu}{to}\mspace{14mu}{test}\mspace{14mu}{peptide}\mspace{14mu}{CPM}}{{Proliferation}\mspace{14mu}{in}\mspace{20mu}{untreated}\mspace{14mu}{wells}\mspace{14mu}{CPM}}$

Mapping T cell epitopes in the IFNβ sequence using the T cellproliferation assay resulted in the identification of two immunogenicregions R1 and R2. This was determined by T cell proliferation in sixdonors that responded to peptides in one or more of these regions.Regions 1 and 2 induce T-cell proliferation in certain individuals. Thecumulative response data for the responding individuals is depicted inFIG. 6, and data from individual responders given in FIG. 7. The epitopedata for INFβ and indicating R1 and R2 and the individual peptide/donorresponses is depicted in FIGS. 8 and 9.

EXAMPLE 3

A number of modified IFNβ molecules were made using conventionalrecombinant DNA techniques. A wild-type IFNβ gene was used both as acontrol reagent, and a template from which to derive modified genes bysite-directed mutagenesis. Wild-type and modified genes were insertedinto a eukaryotic expression vector and the recombinant IFNβ proteinsexpressed as fusion protein with the human immunoglobulin constantregion domain. Recombinant proteins were prepared from transientlytransfected human embryonic kidney cells and assayed as detailed inEXAMPLE 4.

In order to obtain expression from human embryonic kidney cells, thewild-type human IFNβ□ gene was obtained from the ATTCC (ATCC accession #31902) and PCR cloned into vector pd-Cs [Lo, et al (1998), ProteinEngineering 11:495]. The pd-Cs vector directs the expression of a fusionprotein containing the human immunoglobulin constant region domain. Thepd-Cs vector containing the wild-type IFNβ gene was termed pdCs IFNβWT.

Single or multiple codon mutations to generate modified IFNβ genes wasconducted by mutagenic PCR using pdCsIFNβWT as a template. Overlap PCRwas used to combine the two mutated halves of the interferon sequence.The PCR product of 503 bp was digested with XmaI and BamHI, purifiedusing a QIAGEN® gel extraction kit (QIAGEN, Crawley, UK) and transferredinto prepared pd-Cs from which the IFNβ sequence had been removed usingXmaI and BamHI. A positive clone was selected and the INFβ sequenceconfirmed by sequence analysis.

Mutagenesis was conducted using flanking primers 0L575 and 0L576 inseparate reactions in combination with specific mutagenic (mis-matched)primers and the pdCs INFβWT template DNA.

OL575 (XmaI) 5′ CTCCCTGTCCCCGGGTATGAG 3′; and (SEQ ID NO:8) OL576(XhoI/BamHI) 5′-CTTATCATGTCTGGATCCCTCGAG-3′. (SEQ ID NO:9)

Reactions were conducted using EXPAND HI FIDELITY™ PCR reagents(Roche,GmbH) and reaction conditions specified by the following cycle:94° C./2′+25 Cycles@94° C./30″, 60° C./30 ″, 72° C./30″+72° C./10′

The products of the separate reactions were joined by PCR in a reactiondriven by primers 0L575 and 0L576 using 15 cycles of PCR as above.

PCR products were gel purified using commercially available kit systems(QIAGEN® gel extraction kit). The desired clones were digested withBamH1 and Xma1 and the purified product ligated into a prepared pd-Csvector. Cloning was conducted using E.coli XL 1-Blue cells (StrategeneEurope) and culture conditions recommended by the supplier. Sequenceconfirmation was conducted on all final vector preparations using 0L575and 0L576 as sequencing primers.

Expression of modified IFNβ3-lahuman IgFc fusion proteins was achievedusing HEK293 human embryonic kidney cell line as the expression host.All DNA for transfection was prepared using the high purity QIAGEN ®midi-prep system and instructions provided by the supplier (QIAGEN,Crawley, UK). DNA is filter sterilised prior to use and quantified bymeasurement of the A260. Concentrations were adjusted to 0.5-1.0 μg/μl.For transient expression, HEK293 were grown using DMEM L-GLUTAMAX™medium (Invitrogen, Paisley, UK) supplemented with 10% FBS and 250 μg/mlGENETICIN® antibiotic. Prior to transfection, cells were collected bytreatment with trypsin and washed using PBS. After 2 cycles of washingcells are taken into fresh medium at a density of 4×10⁵ cells/ml, andplated into multi-well dishes pre-treated with poly-1-lysine to ensuregood cell adhesion. Typically, 2×10 ⁵ cells are added to each well of a48 well plate and the plates incubated overnight at 37° C./5%CO ₂.

Prior to transfection, the medium is replaced in each well and thetransfection mixes added. Transfection is conducted using thelipofectamine reagent and instructions provided by the supplier(Invitrogen, Paisley, UK). Briefly, transfection mixes are preparedcontaining lipofectamine, OPTI-MEM® modified Eagle's medium (Invitrogen,Paisley, UK) and 0.8 μg DNA per well for each expression vectorconstruct. Transfection mixes are added to the cells and the cellsincubated for 4-6 hours. The medium is replaced with 0.5 ml fresh mediaand the cells incubated at 37° C.5%CO₂ Samples were taken after 48 hoursfor analysis by both anti-Fc ELISA and Daudi cell proliferation assay.The media was harvested after 7 days and stored at 4° C. for furtheranalysis as above.

The medium is assayed for the presence of IFNβ using an ELISA detectingthe human immunglobulin constant region domain of the IFNβ-fusionprotein. For this assay a mouse anti-human IgG Fc preparation (Sigma,Poole, UK) is used as a capture reagent. The IFNβ-HuFc fusion isquantitated with reference to a standard curve generated using adilution series of a reference human IgG preparation (Sigma). BoundIFNβ-Fc fusion or the reference protein is detected using an anti-humanIgG peroxidase conjugate (Sigma) and Sigma OPD colourimetric substrate.

Following estimation of the amount of IFNβ in the HEK.293 conditionedmedium, the conditioned medium is used directly to test the functionalactivity of the modified IFNβ using the anti-proliferation assay asdetailed in EXAMPLE 4.

EXAMPLE 4

Modified interferon molecules of the present invention were tested fortheir ability to inhibit the growth of human B cell lymphoma line Daudi.The method is broadly as described previously [Mark, D. F. et al (1984)Proc. Natl. Acad. Sci. USA 81: 5662-5666] and involves incubation ofDaudi cells with the test interferon. The anti-proliferative effect ofthe test molecule is measured using a soluble dye substance thatundergoes a colour change in the presence of proliferating cells. Theinduced colour change is measured in a spectrophotometer and anyanti-proliferation effect is computed with reference to the colourchange recorded in non-treated control cells and cells treated with astandard interferon preparation.

Briefly, Daudi cells (ATCC # CCL-213) were cultured RPMI 1640 Mediasupplemented with 100 units/ml Penicillin/100 ug/ml Streptomycin and 2mM L-Glutamine and 20% Fetal Bovine Serum (FBS). All media andsupplements were from Gibco (Paisley, UK). The day before assay, cellsare replaced into fresh medium at a density 0.9×10⁶/ml and next dayreplaced into fresh medium as above except containing 10%(v/v) FBS. Thecell density is adjusted to be 2×10⁵ cells/ml.

The test and control interferon preparations are diluted into RPMIcontaining 10% FBS. Dilutions are made into 96-well flat bottom platesto contain 100 ul well and all samples are set up in triplicate.Typically doubling dilution series are set out across each plate.Positive control wells are also included in triplicate with a startingconcentration of the interferon standard (R&D Systems, Abingdon, UK) at20000 pg/ml. Control wells containing 100 ul media alone (no interferon)are also included. 100 ul of the cells are added to each well, and theplates incubated for 72 hours at 37° C., 5% CO₂.

Proliferation is assessed using AQUEOUS ONE™ reagent system and thesuppliers recommended protocol (Promega, Southampton, UK). Briefly, 40μl of the AQUEOUS ONE™ reagent is added to all wells and the substratemixed. Plates are incubated at 37° C. for one hour, and then transferredto the plate reading instrument for determination of the lightabsorbance. Readings are taken at 490 nm. Average absorbance at 490 nmis plotted on the Y axis versus concentrations of interferon standardadded along the X axis. Interferon concentration is determined using anELISA technique as detailed in EXAMPLE 3. For each mutant, the IFNβ-1 aconcentration required to achieve 50% inhibition of cell growth (EC50)was determined from the plot of absorbance versus concentration.

1. A modified human interferon beta (INFβ) which is less immunogenicthan human INFβ (SEQ ID NO: 1) when administered in vivo to a human;wherein the modified human INFβ comprises an amino acid residue sequencethat differs from SEQ ID NO: 1 by amino acid residue substitutions atresidue 57 and residue 67: where the substitution at residue 57 isselected from the group consisting of L57A, L57C, LS57D, L57E, L57G,L57H, L7K, L57N, L57P, L570, L570 , L75R, L57S, and L57T, and thesubstitution at residue 67 is selected from the group consisting ofF67A, F67C, F67D, F67E, F67G, F67H, F67K, F67N, F67P, F67O, F67R, F67S,and F67T.
 2. The modified human INFβ of claim 1 wherein the substitutionat residue 57 is L57A and the substitution at residue 67 is F67H.
 3. Themodified INFβ of claim 2 further comprising one or more additionalsubstitutions in SEQ ID NO: 1 selected from the group consisting ofF50A, I58A, Y60N, M62A, L63A, I66T, I69A, F70A, Y125A, Y126A, I129A,L130A, Y132S, L33A, Y138H, and Y138A.